Starting phenix.real_space_refine
on Fri Aug 22 12:39:11 2025 by dcliebschner
===============================================================================

Processing files:
-------------------------------------------------------------------------------

  Found model, /net/cci-nas-00/data/ceres_data/8zfd_60057/08_2025/8zfd_60057.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8zfd_60057/08_2025/8zfd_60057.map

Processing PHIL parameters:
-------------------------------------------------------------------------------

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.56
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8zfd_60057/08_2025/8zfd_60057.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8zfd_60057/08_2025/8zfd_60057.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8zfd_60057/08_2025/8zfd_60057.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8zfd_60057/08_2025/8zfd_60057.cif"
  }
  resolution = 2.56
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.014
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      13      5.16       5
     C    1475      2.51       5
     N     373      2.21       5
     O     370      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 2231
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "R"
      Number of atoms: 2231
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 294, 2231
          Classifications: {'peptide': 294}
          Incomplete info: {'truncation_to_alanine': 38}
          Link IDs: {'PTRANS': 12, 'TRANS': 281}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 160
          Unresolved non-hydrogen angles: 200
          Unresolved non-hydrogen dihedrals: 137
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'ARG:plan': 8, 'ASP:plan': 4, 'PHE:plan': 2, 'GLU:plan': 5, 'ASN:plan1': 3, 'TYR:plan': 1, 'TRP:plan': 1, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 114
  Time building chain proxies: 0.94, per 1000 atoms: 0.42
  Number of scatterers: 2231
  At special positions: 0
  Unit cell: (61.48, 66.78, 69.96, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      13     16.00
     O     370      8.00
     N     373      7.00
     C    1475      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS R  92 " - pdb=" SG  CYS R 170 " distance=2.05

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.20
  Conformation dependent library (CDL) restraints added in 86.9 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  584 Ramachandran restraints generated.
    292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  564

  Finding SS restraints...
    Secondary structure from input PDB file:
      14 helices and 0 sheets defined
      80.3% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.09
  Creating SS restraints...
    Processing helix  chain 'R' and resid 20 through 50
      removed outlier: 3.602A  pdb=" N   PHE R  28 " --> pdb=" O   SER R  24 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   LEU R  34 " --> pdb=" O   ILE R  30 " (cutoff:3.500A)
      Proline residue:  R  35  - end of helix
      removed outlier: 3.705A  pdb=" N   GLN R  50 " --> pdb=" O   ARG R  46 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 53 through 70
      removed outlier: 3.935A  pdb=" N   TYR R  57 " --> pdb=" O   GLU R  53 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 71 through 81
      removed outlier: 4.155A  pdb=" N   TRP R  75 " --> pdb=" O   THR R  71 " (cutoff:3.500A)
      removed outlier: 3.991A  pdb=" N   ASP R  77 " --> pdb=" O   PRO R  73 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 87 through 101
      removed outlier: 3.696A  pdb=" N   SER R  91 " --> pdb=" O   HIS R  87 " (cutoff:3.500A)
      removed outlier: 4.039A  pdb=" N   CYS R  92 " --> pdb=" O   GLY R  88 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   GLY R  96 " --> pdb=" O   CYS R  92 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   PHE R  97 " --> pdb=" O   LYS R  93 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 102 through 123
      removed outlier: 3.681A  pdb=" N   ALA R 108 " --> pdb=" O   TYR R 104 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   CYS R 111 " --> pdb=" O   ILE R 107 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 132 through 146
    Processing helix  chain 'R' and resid 152 through 157
      removed outlier: 3.580A  pdb=" N   HIS R 157 " --> pdb=" O   PRO R 154 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 177 through 191
      removed outlier: 3.634A  pdb=" N   ALA R 181 " --> pdb=" O   GLU R 177 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   TRP R 182 " --> pdb=" O   ARG R 178 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 192 through 213
      removed outlier: 3.889A  pdb=" N   SER R 212 " --> pdb=" O   ARG R 208 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   SER R 213 " --> pdb=" O   ALA R 209 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 219 through 256
      removed outlier: 3.677A  pdb=" N   SER R 230 " --> pdb=" O   ARG R 226 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   ILE R 232 " --> pdb=" O   ALA R 228 " (cutoff:3.500A)
      removed outlier: 3.810A  pdb=" N   VAL R 235 " --> pdb=" O   LEU R 231 " (cutoff:3.500A)
      removed outlier: 3.842A  pdb=" N   LEU R 236 " --> pdb=" O   ILE R 232 " (cutoff:3.500A)
      Proline residue:  R 241  - end of helix
      removed outlier: 4.060A  pdb=" N   TYR R 253 " --> pdb=" O   ARG R 249 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   LEU R 254 " --> pdb=" O   SER R 250 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 260 through 277
      removed outlier: 3.712A  pdb=" N   GLU R 264 " --> pdb=" O   CYS R 260 " (cutoff:3.500A)
      removed outlier: 4.130A  pdb=" N   ARG R 265 " --> pdb=" O   GLY R 261 " (cutoff:3.500A)
      removed outlier: 5.077A  pdb=" N   SER R 268 " --> pdb=" O   GLU R 264 " (cutoff:3.500A)
      removed outlier: 5.119A  pdb=" N   ALA R 269 " --> pdb=" O   ARG R 265 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 278 through 280
      No H-bonds generated for 'chain 'R' and resid 278 through 280'
    Processing helix  chain 'R' and resid 282 through 290
      removed outlier: 3.811A  pdb=" N   ILE R 286 " --> pdb=" O   VAL R 282 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 292 through 304

    148 hydrogen bonds defined for protein.
    438 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.32

  Time building geometry restraints manager: 0.27 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.21 -     1.33: 418
        1.33 -     1.45: 613
        1.45 -     1.57: 1249
        1.57 -     1.69: 0
        1.69 -     1.82: 17
  Bond restraints: 2297
  Sorted by residual:
  bond pdb=" CA  CYS R 170 "
       pdb=" C   CYS R 170 "
    ideal  model  delta    sigma   weight residual
    1.520  1.489  0.031 1.12e-02 7.97e+03 7.46e+00
  bond pdb=" CA  PHE R 174 "
       pdb=" CB  PHE R 174 "
    ideal  model  delta    sigma   weight residual
    1.530  1.489  0.041 1.58e-02 4.01e+03 6.62e+00
  bond pdb=" C   CYS R 170 "
       pdb=" O   CYS R 170 "
    ideal  model  delta    sigma   weight residual
    1.235  1.206  0.028 1.18e-02 7.18e+03 5.73e+00
  bond pdb=" CA  GLU R 172 "
       pdb=" CB  GLU R 172 "
    ideal  model  delta    sigma   weight residual
    1.534  1.500  0.034 1.57e-02 4.06e+03 4.58e+00
  bond pdb=" C   PHE R 174 "
       pdb=" N   PRO R 175 "
    ideal  model  delta    sigma   weight residual
    1.334  1.287  0.047 2.34e-02 1.83e+03 4.09e+00
  ... (remaining 2292 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.82: 3118
        3.82 -     7.64: 24
        7.64 -    11.47: 2
       11.47 -    15.29: 2
       15.29 -    19.11: 1
  Bond angle restraints: 3147
  Sorted by residual:
  angle pdb=" N   LYS R 173 "
        pdb=" CA  LYS R 173 "
        pdb=" C   LYS R 173 "
      ideal   model   delta    sigma   weight residual
     110.80   91.69   19.11 2.13e+00 2.20e-01 8.05e+01
  angle pdb=" C   LYS R 173 "
        pdb=" CA  LYS R 173 "
        pdb=" CB  LYS R 173 "
      ideal   model   delta    sigma   weight residual
     110.42  124.89  -14.47 1.99e+00 2.53e-01 5.29e+01
  angle pdb=" C   PHE R 174 "
        pdb=" CA  PHE R 174 "
        pdb=" CB  PHE R 174 "
      ideal   model   delta    sigma   weight residual
     110.17  121.65  -11.48 1.97e+00 2.58e-01 3.39e+01
  angle pdb=" N   CYS R 170 "
        pdb=" CA  CYS R 170 "
        pdb=" C   CYS R 170 "
      ideal   model   delta    sigma   weight residual
     108.13  100.51    7.62 1.72e+00 3.38e-01 1.96e+01
  angle pdb=" C   GLU R 172 "
        pdb=" N   LYS R 173 "
        pdb=" CA  LYS R 173 "
      ideal   model   delta    sigma   weight residual
     121.54  129.27   -7.73 1.91e+00 2.74e-01 1.64e+01
  ... (remaining 3142 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    13.26: 1117
       13.26 -    26.52: 158
       26.52 -    39.78: 31
       39.78 -    53.03: 8
       53.03 -    66.29: 2
  Dihedral angle restraints: 1316
    sinusoidal: 445
      harmonic: 871
  Sorted by residual:
  dihedral pdb=" CB  CYS R  92 "
           pdb=" SG  CYS R  92 "
           pdb=" SG  CYS R 170 "
           pdb=" CB  CYS R 170 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  145.43  -52.43     1      1.00e+01 1.00e-02 3.75e+01
  dihedral pdb=" C   PHE R 174 "
           pdb=" N   PHE R 174 "
           pdb=" CA  PHE R 174 "
           pdb=" CB  PHE R 174 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -135.40   12.80     0      2.50e+00 1.60e-01 2.62e+01
  dihedral pdb=" CA  THR R 216 "
           pdb=" C   THR R 216 "
           pdb=" N   GLU R 217 "
           pdb=" CA  GLU R 217 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.97  -25.03     0      5.00e+00 4.00e-02 2.51e+01
  ... (remaining 1313 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.089: 331
       0.089 -    0.177: 34
       0.177 -    0.266: 1
       0.266 -    0.354: 0
       0.354 -    0.443: 1
  Chirality restraints: 367
  Sorted by residual:
  chirality pdb=" CA  PHE R 174 "
            pdb=" N   PHE R 174 "
            pdb=" C   PHE R 174 "
            pdb=" CB  PHE R 174 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.07    0.44 2.00e-01 2.50e+01 4.90e+00
  chirality pdb=" CA  PHE R 171 "
            pdb=" N   PHE R 171 "
            pdb=" C   PHE R 171 "
            pdb=" CB  PHE R 171 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 1.01e+00
  chirality pdb=" CA  CYS R 170 "
            pdb=" N   CYS R 170 "
            pdb=" C   CYS R 170 "
            pdb=" CB  CYS R 170 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.68   -0.17 2.00e-01 2.50e+01 7.18e-01
  ... (remaining 364 not shown)

  Planarity restraints: 389
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE R 174 "   -0.053 5.00e-02 4.00e+02   7.99e-02 1.02e+01
        pdb=" N   PRO R 175 "    0.138 5.00e-02 4.00e+02
        pdb=" CA  PRO R 175 "   -0.041 5.00e-02 4.00e+02
        pdb=" CD  PRO R 175 "   -0.044 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE R 174 "    0.027 2.00e-02 2.50e+03   2.26e-02 8.91e+00
        pdb=" CG  PHE R 174 "   -0.052 2.00e-02 2.50e+03
        pdb=" CD1 PHE R 174 "    0.004 2.00e-02 2.50e+03
        pdb=" CD2 PHE R 174 "    0.006 2.00e-02 2.50e+03
        pdb=" CE1 PHE R 174 "    0.008 2.00e-02 2.50e+03
        pdb=" CE2 PHE R 174 "    0.006 2.00e-02 2.50e+03
        pdb=" CZ  PHE R 174 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN R 102 "    0.014 2.00e-02 2.50e+03   2.83e-02 7.99e+00
        pdb=" C   ASN R 102 "   -0.049 2.00e-02 2.50e+03
        pdb=" O   ASN R 102 "    0.018 2.00e-02 2.50e+03
        pdb=" N   ILE R 103 "    0.017 2.00e-02 2.50e+03
  ... (remaining 386 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.75: 380
        2.75 -     3.29: 2172
        3.29 -     3.83: 3795
        3.83 -     4.36: 4370
        4.36 -     4.90: 7602
  Nonbonded interactions: 18319
  Sorted by model distance:
  nonbonded pdb=" OH  TYR R  45 "
            pdb=" NH2 ARG R  49 "
     model   vdw
     2.217 3.120
  nonbonded pdb=" OD1 ASN R  60 "
            pdb=" NE1 TRP R 144 "
     model   vdw
     2.279 3.120
  nonbonded pdb=" O   LEU R  20 "
            pdb=" OG  SER R  24 "
     model   vdw
     2.382 3.040
  nonbonded pdb=" O   GLY R 149 "
            pdb=" OG  SER R 152 "
     model   vdw
     2.443 3.040
  nonbonded pdb=" N   LYS R 173 "
            pdb=" O   LYS R 173 "
     model   vdw
     2.452 2.496
  ... (remaining 18314 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.070
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.040
  Check model and map are aligned:         0.010
  Set scattering table:                    0.000
  Process input model:                     5.260
  Find NCS groups from input model:        0.000
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:7.630
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.020
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7264
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.047   2298  Z= 0.301
  Angle     :  0.985  19.110   3149  Z= 0.533
  Chirality :  0.055   0.443    367
  Planarity :  0.006   0.080    389
  Dihedral  : 13.008  66.293    749
  Min Nonbonded Distance : 2.217

Molprobity Statistics.
  All-atom Clashscore : 9.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.93 %
    Favored  : 90.07 %
  Rotamer:
    Outliers :  0.46 %
    Allowed  :  0.92 %
    Favored  : 98.62 %
  Cbeta Deviations :  0.71 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.61 (0.48), residues: 292
  helix: -0.04 (0.37), residues: 202
  sheet:  None (None), residues: 0
  loop : -3.46 (0.54), residues: 90

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG R 126 
 TYR   0.026   0.003   TYR R 104 
 PHE   0.052   0.003   PHE R 174 
 TRP   0.010   0.002   TRP R  75 
 HIS   0.004   0.002   HIS R 157 

Details of bonding type rmsd
  covalent geometry    : bond        0.00655 ( 2297)
  covalent geometry    : angle       0.98362 ( 3147)
  SS BOND              : bond        0.02350 (    1)
  SS BOND              : angle       2.57596 (    2)
  hydrogen bonds       : bond        0.11613 (  148)
  hydrogen bonds       : angle       6.48963 (  438)

*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  584 Ramachandran restraints generated.
    292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  584 Ramachandran restraints generated.
    292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  38 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 37
  time to evaluate  : 0.086 
Fit side-chains
REVERT: R   83 ASP cc_start: 0.6430 (m-30) cc_final: 0.6117 (m-30)
  outliers start: 1
  outliers final: 0
  residues processed: 38
  average time/residue: 0.6240
  time to fit residues: 24.2015
Evaluate side-chains
  29 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 29
  time to evaluate  : 0.082 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 29
   random chunks:
   chunk 27 optimal weight:    0.9980
   chunk 12 optimal weight:    0.6980
   chunk 24 optimal weight:    3.9990
   chunk 28 optimal weight:    0.5980
   chunk 13 optimal weight:    0.9980
   chunk 1 optimal weight:    0.4980
   chunk 8 optimal weight:    0.7980
   chunk 16 optimal weight:    0.5980
   chunk 15 optimal weight:    0.9990
   chunk 25 optimal weight:    0.6980
   chunk 26 optimal weight:    0.6980
   overall best weight:    0.6180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4197 r_free = 0.4197 target = 0.178939 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.128830 restraints weight = 2494.933|
|-----------------------------------------------------------------------------|
r_work (start): 0.3622 rms_B_bonded: 1.59
r_work: 0.3488 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.3372 rms_B_bonded: 3.53 restraints_weight: 0.2500
r_work (final): 0.3372
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7506
moved from start:          0.0969

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.040   2298  Z= 0.238
  Angle     :  0.762   8.423   3149  Z= 0.392
  Chirality :  0.046   0.170    367
  Planarity :  0.005   0.038    389
  Dihedral  :  6.237  28.732    319
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 7.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.90 %
    Favored  : 91.10 %
  Rotamer:
    Outliers :  0.92 %
    Allowed  : 15.21 %
    Favored  : 83.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.29 (0.49), residues: 292
  helix:  0.17 (0.37), residues: 210
  sheet:  None (None), residues: 0
  loop : -3.55 (0.56), residues: 82

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG R 226 
 TYR   0.024   0.003   TYR R 104 
 PHE   0.024   0.002   PHE R 174 
 TRP   0.009   0.002   TRP R  75 
 HIS   0.004   0.001   HIS R 157 

Details of bonding type rmsd
  covalent geometry    : bond        0.00576 ( 2297)
  covalent geometry    : angle       0.76186 ( 3147)
  SS BOND              : bond        0.00083 (    1)
  SS BOND              : angle       1.07389 (    2)
  hydrogen bonds       : bond        0.04311 (  148)
  hydrogen bonds       : angle       5.56893 (  438)

*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  584 Ramachandran restraints generated.
    292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  584 Ramachandran restraints generated.
    292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  36 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 34
  time to evaluate  : 0.087 
Fit side-chains
REVERT: R   83 ASP cc_start: 0.7099 (m-30) cc_final: 0.6655 (m-30)
REVERT: R  274 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8318 (tp)
REVERT: R  292 ASN cc_start: 0.7387 (p0) cc_final: 0.7075 (p0)
  outliers start: 2
  outliers final: 0
  residues processed: 34
  average time/residue: 0.5027
  time to fit residues: 17.5488
Evaluate side-chains
  34 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 33
  time to evaluate  : 0.084 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  274 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 29
   random chunks:
   chunk 19 optimal weight:    0.0980
   chunk 4 optimal weight:    0.5980
   chunk 26 optimal weight:    0.5980
   chunk 24 optimal weight:    1.9990
   chunk 3 optimal weight:    0.5980
   chunk 12 optimal weight:    0.5980
   chunk 11 optimal weight:    0.8980
   chunk 16 optimal weight:    0.3980
   chunk 27 optimal weight:    0.0010
   chunk 15 optimal weight:    2.9990
   chunk 7 optimal weight:    2.9990
   overall best weight:    0.3386

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** R 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4223 r_free = 0.4223 target = 0.181086 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.131314 restraints weight = 2520.197|
|-----------------------------------------------------------------------------|
r_work (start): 0.3655 rms_B_bonded: 1.61
r_work: 0.3522 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.3407 rms_B_bonded: 3.57 restraints_weight: 0.2500
r_work (final): 0.3407
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7464
moved from start:          0.1333

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   2298  Z= 0.154
  Angle     :  0.652   6.785   3149  Z= 0.336
  Chirality :  0.042   0.123    367
  Planarity :  0.004   0.038    389
  Dihedral  :  5.769  28.356    319
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 6.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.53 %
    Favored  : 92.47 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 13.82 %
    Favored  : 82.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.77 (0.49), residues: 292
  helix:  0.56 (0.37), residues: 210
  sheet:  None (None), residues: 0
  loop : -3.38 (0.56), residues: 82

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG R 226 
 TYR   0.020   0.002   TYR R 104 
 PHE   0.027   0.002   PHE R  28 
 TRP   0.009   0.001   TRP R  75 
 HIS   0.002   0.001   HIS R 243 

Details of bonding type rmsd
  covalent geometry    : bond        0.00369 ( 2297)
  covalent geometry    : angle       0.65203 ( 3147)
  SS BOND              : bond        0.00075 (    1)
  SS BOND              : angle       0.82327 (    2)
  hydrogen bonds       : bond        0.03534 (  148)
  hydrogen bonds       : angle       5.27841 (  438)

*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  584 Ramachandran restraints generated.
    292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  584 Ramachandran restraints generated.
    292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 36
  time to evaluate  : 0.089 
Fit side-chains
REVERT: R   49 ARG cc_start: 0.7440 (OUTLIER) cc_final: 0.6654 (tpm-80)
  outliers start: 8
  outliers final: 2
  residues processed: 38
  average time/residue: 0.4575
  time to fit residues: 17.8811
Evaluate side-chains
  35 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 32
  time to evaluate  : 0.092 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   49 ARG
Chi-restraints excluded: chain R residue  211 GLN
Chi-restraints excluded: chain R residue  212 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 29
   random chunks:
   chunk 21 optimal weight:    0.9980
   chunk 25 optimal weight:    0.6980
   chunk 12 optimal weight:    0.7980
   chunk 17 optimal weight:    0.2980
   chunk 11 optimal weight:    0.2980
   chunk 15 optimal weight:    1.9990
   chunk 16 optimal weight:    0.7980
   chunk 14 optimal weight:    0.0970
   chunk 23 optimal weight:    0.6980
   chunk 22 optimal weight:    0.0980
   chunk 28 optimal weight:    0.9980
   overall best weight:    0.2978

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** R 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4227 r_free = 0.4227 target = 0.181748 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.132600 restraints weight = 2503.334|
|-----------------------------------------------------------------------------|
r_work (start): 0.3668 rms_B_bonded: 1.61
r_work: 0.3535 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.3421 rms_B_bonded: 3.54 restraints_weight: 0.2500
r_work (final): 0.3421
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7453
moved from start:          0.1619

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   2298  Z= 0.143
  Angle     :  0.645   6.800   3149  Z= 0.330
  Chirality :  0.042   0.126    367
  Planarity :  0.004   0.038    389
  Dihedral  :  5.559  28.441    319
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 5.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.51 %
    Favored  : 93.49 %
  Rotamer:
    Outliers :  4.61 %
    Allowed  : 14.75 %
    Favored  : 80.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.36 (0.51), residues: 292
  helix:  0.85 (0.37), residues: 210
  sheet:  None (None), residues: 0
  loop : -3.17 (0.60), residues: 82

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG R 226 
 TYR   0.019   0.002   TYR R 104 
 PHE   0.014   0.002   PHE R 174 
 TRP   0.008   0.001   TRP R  75 
 HIS   0.006   0.001   HIS R 157 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 ( 2297)
  covalent geometry    : angle       0.64503 ( 3147)
  SS BOND              : bond        0.00085 (    1)
  SS BOND              : angle       0.79179 (    2)
  hydrogen bonds       : bond        0.03391 (  148)
  hydrogen bonds       : angle       5.16578 (  438)

*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  584 Ramachandran restraints generated.
    292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  584 Ramachandran restraints generated.
    292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 32
  time to evaluate  : 0.070 
Fit side-chains
REVERT: R  152 SER cc_start: 0.8176 (t) cc_final: 0.7511 (p)
  outliers start: 10
  outliers final: 4
  residues processed: 35
  average time/residue: 0.4320
  time to fit residues: 15.5962
Evaluate side-chains
  33 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 29
  time to evaluate  : 0.083 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   13 VAL
Chi-restraints excluded: chain R residue  176 MET
Chi-restraints excluded: chain R residue  212 SER
Chi-restraints excluded: chain R residue  277 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 29
   random chunks:
   chunk 7 optimal weight:    4.9990
   chunk 1 optimal weight:    0.6980
   chunk 2 optimal weight:    0.5980
   chunk 12 optimal weight:    0.9990
   chunk 13 optimal weight:    0.8980
   chunk 20 optimal weight:    0.7980
   chunk 24 optimal weight:    0.0670
   chunk 0 optimal weight:    1.9990
   chunk 4 optimal weight:    0.4980
   chunk 19 optimal weight:    0.2980
   chunk 9 optimal weight:    0.0870
   overall best weight:    0.3096

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** R 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4225 r_free = 0.4225 target = 0.181875 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.132547 restraints weight = 2473.703|
|-----------------------------------------------------------------------------|
r_work (start): 0.3668 rms_B_bonded: 1.61
r_work: 0.3533 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.3417 rms_B_bonded: 3.58 restraints_weight: 0.2500
r_work (final): 0.3417
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7475
moved from start:          0.1724

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   2298  Z= 0.145
  Angle     :  0.640   7.127   3149  Z= 0.325
  Chirality :  0.041   0.130    367
  Planarity :  0.004   0.034    389
  Dihedral  :  5.463  27.967    319
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 6.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.51 %
    Favored  : 93.49 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 19.35 %
    Favored  : 77.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.19 (0.51), residues: 292
  helix:  0.98 (0.37), residues: 210
  sheet:  None (None), residues: 0
  loop : -3.14 (0.62), residues: 82

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG R 187 
 TYR   0.018   0.002   TYR R 104 
 PHE   0.024   0.002   PHE R  28 
 TRP   0.007   0.001   TRP R  75 
 HIS   0.003   0.001   HIS R 157 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 ( 2297)
  covalent geometry    : angle       0.63959 ( 3147)
  SS BOND              : bond        0.00043 (    1)
  SS BOND              : angle       0.71558 (    2)
  hydrogen bonds       : bond        0.03352 (  148)
  hydrogen bonds       : angle       5.14216 (  438)

*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  584 Ramachandran restraints generated.
    292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  584 Ramachandran restraints generated.
    292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  37 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 30
  time to evaluate  : 0.101 
Fit side-chains
REVERT: R  152 SER cc_start: 0.8093 (t) cc_final: 0.7488 (p)
REVERT: R  274 LEU cc_start: 0.8561 (tm) cc_final: 0.8306 (tp)
  outliers start: 7
  outliers final: 5
  residues processed: 34
  average time/residue: 0.4466
  time to fit residues: 15.6487
Evaluate side-chains
  34 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 29
  time to evaluate  : 0.081 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   13 VAL
Chi-restraints excluded: chain R residue  146 THR
Chi-restraints excluded: chain R residue  176 MET
Chi-restraints excluded: chain R residue  212 SER
Chi-restraints excluded: chain R residue  277 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 29
   random chunks:
   chunk 9 optimal weight:    0.2980
   chunk 24 optimal weight:    0.0170
   chunk 12 optimal weight:    0.7980
   chunk 10 optimal weight:    0.2980
   chunk 14 optimal weight:    0.9980
   chunk 23 optimal weight:    0.5980
   chunk 3 optimal weight:    0.6980
   chunk 21 optimal weight:    0.4980
   chunk 2 optimal weight:    0.8980
   chunk 26 optimal weight:    0.9990
   chunk 27 optimal weight:    0.3980
   overall best weight:    0.3018

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** R 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4228 r_free = 0.4228 target = 0.182154 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.132628 restraints weight = 2458.946|
|-----------------------------------------------------------------------------|
r_work (start): 0.3672 rms_B_bonded: 1.61
r_work: 0.3539 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.3423 rms_B_bonded: 3.57 restraints_weight: 0.2500
r_work (final): 0.3423
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7448
moved from start:          0.1872

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   2298  Z= 0.142
  Angle     :  0.638   6.876   3149  Z= 0.322
  Chirality :  0.041   0.129    367
  Planarity :  0.004   0.036    389
  Dihedral  :  5.404  28.440    319
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 5.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.82 %
    Favored  : 94.18 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 18.89 %
    Favored  : 77.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.09 (0.52), residues: 292
  helix:  0.98 (0.37), residues: 216
  sheet:  None (None), residues: 0
  loop : -3.17 (0.67), residues: 76

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG R 187 
 TYR   0.017   0.002   TYR R 104 
 PHE   0.013   0.002   PHE R 174 
 TRP   0.006   0.001   TRP R  75 
 HIS   0.003   0.001   HIS R 157 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 ( 2297)
  covalent geometry    : angle       0.63833 ( 3147)
  SS BOND              : bond        0.00034 (    1)
  SS BOND              : angle       0.68556 (    2)
  hydrogen bonds       : bond        0.03304 (  148)
  hydrogen bonds       : angle       5.12429 (  438)

*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  584 Ramachandran restraints generated.
    292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  584 Ramachandran restraints generated.
    292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 31
  time to evaluate  : 0.088 
Fit side-chains
REVERT: R   51 HIS cc_start: 0.7667 (OUTLIER) cc_final: 0.6607 (m90)
REVERT: R   80 LEU cc_start: 0.7888 (mt) cc_final: 0.7656 (mt)
REVERT: R  152 SER cc_start: 0.8104 (t) cc_final: 0.7447 (p)
REVERT: R  274 LEU cc_start: 0.8463 (tm) cc_final: 0.8207 (tp)
  outliers start: 8
  outliers final: 5
  residues processed: 35
  average time/residue: 0.3812
  time to fit residues: 13.7691
Evaluate side-chains
  37 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 31
  time to evaluate  : 0.081 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   13 VAL
Chi-restraints excluded: chain R residue   51 HIS
Chi-restraints excluded: chain R residue  146 THR
Chi-restraints excluded: chain R residue  176 MET
Chi-restraints excluded: chain R residue  212 SER
Chi-restraints excluded: chain R residue  277 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 29
   random chunks:
   chunk 3 optimal weight:    0.5980
   chunk 25 optimal weight:    1.9990
   chunk 26 optimal weight:    0.5980
   chunk 2 optimal weight:    0.6980
   chunk 18 optimal weight:    0.0980
   chunk 1 optimal weight:    0.2980
   chunk 13 optimal weight:    0.2980
   chunk 6 optimal weight:    0.0980
   chunk 7 optimal weight:    0.9990
   chunk 0 optimal weight:    0.9980
   chunk 21 optimal weight:    0.1980
   overall best weight:    0.1980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** R 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4242 r_free = 0.4242 target = 0.183810 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.134490 restraints weight = 2474.394|
|-----------------------------------------------------------------------------|
r_work (start): 0.3691 rms_B_bonded: 1.61
r_work: 0.3557 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.3444 rms_B_bonded: 3.59 restraints_weight: 0.2500
r_work (final): 0.3444
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7439
moved from start:          0.2035

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   2298  Z= 0.119
  Angle     :  0.600   6.210   3149  Z= 0.303
  Chirality :  0.040   0.131    367
  Planarity :  0.004   0.035    389
  Dihedral  :  5.190  27.369    319
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 6.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.82 %
    Favored  : 94.18 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 19.82 %
    Favored  : 76.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.10 (0.52), residues: 292
  helix:  1.09 (0.37), residues: 218
  sheet:  None (None), residues: 0
  loop : -3.10 (0.67), residues: 74

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG R 187 
 TYR   0.015   0.001   TYR R 104 
 PHE   0.023   0.002   PHE R  28 
 TRP   0.006   0.001   TRP R  75 
 HIS   0.003   0.001   HIS R 157 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 2297)
  covalent geometry    : angle       0.59991 ( 3147)
  SS BOND              : bond        0.00023 (    1)
  SS BOND              : angle       0.60090 (    2)
  hydrogen bonds       : bond        0.02988 (  148)
  hydrogen bonds       : angle       4.99785 (  438)

*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  584 Ramachandran restraints generated.
    292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  584 Ramachandran restraints generated.
    292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 33
  time to evaluate  : 0.120 
Fit side-chains
REVERT: R  274 LEU cc_start: 0.8444 (tm) cc_final: 0.8175 (tp)
  outliers start: 8
  outliers final: 5
  residues processed: 37
  average time/residue: 0.2883
  time to fit residues: 11.0240
Evaluate side-chains
  35 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 30
  time to evaluate  : 0.080 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   13 VAL
Chi-restraints excluded: chain R residue  146 THR
Chi-restraints excluded: chain R residue  176 MET
Chi-restraints excluded: chain R residue  212 SER
Chi-restraints excluded: chain R residue  277 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 29
   random chunks:
   chunk 28 optimal weight:    0.9990
   chunk 21 optimal weight:    0.2980
   chunk 13 optimal weight:    2.9990
   chunk 1 optimal weight:    0.5980
   chunk 10 optimal weight:    0.0870
   chunk 11 optimal weight:    0.0170
   chunk 3 optimal weight:    0.8980
   chunk 20 optimal weight:    0.0030
   chunk 27 optimal weight:    0.5980
   chunk 24 optimal weight:    0.0070
   chunk 22 optimal weight:    0.0980
   overall best weight:    0.0424

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
R  81 HIS
R 102 ASN
R 271 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4299 r_free = 0.4299 target = 0.189587 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.141150 restraints weight = 2466.006|
|-----------------------------------------------------------------------------|
r_work (start): 0.3777 rms_B_bonded: 1.61
r_work: 0.3647 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.3536 rms_B_bonded: 3.62 restraints_weight: 0.2500
r_work (final): 0.3536
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7332
moved from start:          0.2831

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   2298  Z= 0.104
  Angle     :  0.598   8.730   3149  Z= 0.292
  Chirality :  0.039   0.121    367
  Planarity :  0.004   0.035    389
  Dihedral  :  4.698  25.126    319
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 5.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.79 %
    Favored  : 95.21 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 21.66 %
    Favored  : 74.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.39 (0.52), residues: 292
  helix:  1.39 (0.37), residues: 217
  sheet:  None (None), residues: 0
  loop : -3.28 (0.64), residues: 75

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG R 187 
 TYR   0.015   0.001   TYR R 104 
 PHE   0.010   0.001   PHE R 174 
 TRP   0.005   0.001   TRP R 182 
 HIS   0.005   0.001   HIS R  81 

Details of bonding type rmsd
  covalent geometry    : bond        0.00227 ( 2297)
  covalent geometry    : angle       0.59849 ( 3147)
  SS BOND              : bond        0.00003 (    1)
  SS BOND              : angle       0.54775 (    2)
  hydrogen bonds       : bond        0.02453 (  148)
  hydrogen bonds       : angle       4.69840 (  438)

*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  584 Ramachandran restraints generated.
    292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  584 Ramachandran restraints generated.
    292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 32
  time to evaluate  : 0.050 
Fit side-chains
REVERT: R   80 LEU cc_start: 0.7904 (mt) cc_final: 0.7538 (mt)
REVERT: R  274 LEU cc_start: 0.8324 (tm) cc_final: 0.8071 (tp)
  outliers start: 8
  outliers final: 3
  residues processed: 37
  average time/residue: 0.2660
  time to fit residues: 10.1377
Evaluate side-chains
  28 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 25
  time to evaluate  : 0.047 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   13 VAL
Chi-restraints excluded: chain R residue  146 THR
Chi-restraints excluded: chain R residue  277 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 29
   random chunks:
   chunk 6 optimal weight:    0.5980
   chunk 24 optimal weight:    0.8980
   chunk 16 optimal weight:    0.1980
   chunk 23 optimal weight:    0.8980
   chunk 17 optimal weight:    0.1980
   chunk 7 optimal weight:    0.7980
   chunk 11 optimal weight:    0.1980
   chunk 27 optimal weight:    0.0060
   chunk 14 optimal weight:    0.1980
   chunk 9 optimal weight:    0.3980
   chunk 20 optimal weight:    0.4980
   overall best weight:    0.1596

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
R  81 HIS
R 271 HIS
R 292 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4289 r_free = 0.4289 target = 0.185992 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.137290 restraints weight = 2459.076|
|-----------------------------------------------------------------------------|
r_work (start): 0.3739 rms_B_bonded: 1.60
r_work: 0.3596 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.3473 rms_B_bonded: 3.68 restraints_weight: 0.2500
r_work (final): 0.3473
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7412
moved from start:          0.2771

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   2298  Z= 0.113
  Angle     :  0.602   6.352   3149  Z= 0.302
  Chirality :  0.039   0.118    367
  Planarity :  0.004   0.034    389
  Dihedral  :  4.789  25.705    319
  Min Nonbonded Distance : 2.616

Molprobity Statistics.
  All-atom Clashscore : 5.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.79 %
    Favored  : 95.21 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 22.58 %
    Favored  : 73.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.63 (0.53), residues: 292
  helix:  1.54 (0.37), residues: 218
  sheet:  None (None), residues: 0
  loop : -3.16 (0.65), residues: 74

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG R 126 
 TYR   0.014   0.001   TYR R 104 
 PHE   0.025   0.002   PHE R  28 
 TRP   0.005   0.001   TRP R  42 
 HIS   0.005   0.001   HIS R  81 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 ( 2297)
  covalent geometry    : angle       0.60193 ( 3147)
  SS BOND              : bond        0.00057 (    1)
  SS BOND              : angle       0.56795 (    2)
  hydrogen bonds       : bond        0.02892 (  148)
  hydrogen bonds       : angle       4.74820 (  438)

*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  584 Ramachandran restraints generated.
    292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  584 Ramachandran restraints generated.
    292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 31
  time to evaluate  : 0.051 
Fit side-chains
REVERT: R   80 LEU cc_start: 0.7927 (mt) cc_final: 0.7548 (mt)
REVERT: R  274 LEU cc_start: 0.8353 (tm) cc_final: 0.8085 (tp)
  outliers start: 8
  outliers final: 4
  residues processed: 36
  average time/residue: 0.2657
  time to fit residues: 9.8989
Evaluate side-chains
  32 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 28
  time to evaluate  : 0.048 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   13 VAL
Chi-restraints excluded: chain R residue  146 THR
Chi-restraints excluded: chain R residue  183 MET
Chi-restraints excluded: chain R residue  277 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 29
   random chunks:
   chunk 25 optimal weight:    0.4980
   chunk 26 optimal weight:    0.3980
   chunk 6 optimal weight:    0.7980
   chunk 4 optimal weight:    0.8980
   chunk 12 optimal weight:    0.5980
   chunk 19 optimal weight:    0.3980
   chunk 21 optimal weight:    0.0770
   chunk 24 optimal weight:    0.0060
   chunk 13 optimal weight:    0.3980
   chunk 22 optimal weight:    0.0270
   chunk 0 optimal weight:    5.9990
   overall best weight:    0.1812

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
R  81 HIS
R 271 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4285 r_free = 0.4285 target = 0.185750 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.137156 restraints weight = 2496.694|
|-----------------------------------------------------------------------------|
r_work (start): 0.3728 rms_B_bonded: 1.61
r_work: 0.3594 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.3476 rms_B_bonded: 3.63 restraints_weight: 0.2500
r_work (final): 0.3476
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7438
moved from start:          0.2789

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   2298  Z= 0.116
  Angle     :  0.592   6.509   3149  Z= 0.302
  Chirality :  0.040   0.119    367
  Planarity :  0.004   0.034    389
  Dihedral  :  4.850  26.216    319
  Min Nonbonded Distance : 2.623

Molprobity Statistics.
  All-atom Clashscore : 5.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.79 %
    Favored  : 95.21 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 24.42 %
    Favored  : 71.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.65 (0.53), residues: 292
  helix:  1.48 (0.37), residues: 220
  sheet:  None (None), residues: 0
  loop : -3.03 (0.67), residues: 72

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG R 126 
 TYR   0.015   0.001   TYR R 104 
 PHE   0.014   0.001   PHE R 174 
 TRP   0.005   0.001   TRP R  42 
 HIS   0.005   0.001   HIS R  81 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 ( 2297)
  covalent geometry    : angle       0.59215 ( 3147)
  SS BOND              : bond        0.00038 (    1)
  SS BOND              : angle       0.55836 (    2)
  hydrogen bonds       : bond        0.02996 (  148)
  hydrogen bonds       : angle       4.79165 (  438)

********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  584 Ramachandran restraints generated.
    292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  584 Ramachandran restraints generated.
    292 Oldfield, 0 Emsley, 292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  37 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 29
  time to evaluate  : 0.083 
Fit side-chains
REVERT: R   80 LEU cc_start: 0.8032 (mt) cc_final: 0.7707 (mt)
REVERT: R  274 LEU cc_start: 0.8383 (tm) cc_final: 0.8110 (tp)
  outliers start: 8
  outliers final: 5
  residues processed: 34
  average time/residue: 0.3830
  time to fit residues: 13.4373
Evaluate side-chains
  34 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 29
  time to evaluate  : 0.086 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   13 VAL
Chi-restraints excluded: chain R residue  146 THR
Chi-restraints excluded: chain R residue  183 MET
Chi-restraints excluded: chain R residue  212 SER
Chi-restraints excluded: chain R residue  277 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 29
   random chunks:
   chunk 14 optimal weight:    0.7980
   chunk 12 optimal weight:    0.0970
   chunk 2 optimal weight:    0.6980
   chunk 4 optimal weight:    0.9980
   chunk 17 optimal weight:    0.5980
   chunk 24 optimal weight:    2.9990
   chunk 26 optimal weight:    0.2980
   chunk 3 optimal weight:    0.7980
   chunk 7 optimal weight:    2.9990
   chunk 1 optimal weight:    0.6980
   chunk 16 optimal weight:    0.8980
   overall best weight:    0.4778

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
R  81 HIS
R 271 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4238 r_free = 0.4238 target = 0.180662 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.131719 restraints weight = 2441.548|
|-----------------------------------------------------------------------------|
r_work (start): 0.3669 rms_B_bonded: 1.57
r_work: 0.3526 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.3404 rms_B_bonded: 3.57 restraints_weight: 0.2500
r_work (final): 0.3404
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7493
moved from start:          0.2370

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035   2298  Z= 0.189
  Angle     :  0.652   6.184   3149  Z= 0.336
  Chirality :  0.043   0.126    367
  Planarity :  0.005   0.035    389
  Dihedral  :  5.340  28.803    319
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 6.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.82 %
    Favored  : 94.18 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 23.96 %
    Favored  : 72.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.33 (0.52), residues: 292
  helix:  1.15 (0.37), residues: 221
  sheet:  None (None), residues: 0
  loop : -2.84 (0.66), residues: 71

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG R 126 
 TYR   0.017   0.002   TYR R 104 
 PHE   0.026   0.002   PHE R  28 
 TRP   0.008   0.001   TRP R  42 
 HIS   0.004   0.001   HIS R  81 

Details of bonding type rmsd
  covalent geometry    : bond        0.00459 ( 2297)
  covalent geometry    : angle       0.65207 ( 3147)
  SS BOND              : bond        0.00015 (    1)
  SS BOND              : angle       0.63785 (    2)
  hydrogen bonds       : bond        0.03805 (  148)
  hydrogen bonds       : angle       5.15493 (  438)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1264.31 seconds
wall clock time: 22 minutes 21.09 seconds (1341.09 seconds total)